PIK3CA c.1037T>G, p.Val346Gly

Reasoning

The VCEP requires PM2 before phenotype points can be used. The variant is reported absent from gnomAD v2.1 and v4.1, satisfying the available PM2 prerequisite. The governing Table 2A assigns 0.25 points for each separate tumor occurrence; COSMIC reports this exact variant (PIK3CA c.1037T>G / p.Val346Gly / p.V346G) two times, so the calculated score is 0.25 + 0.25 = 0.50 points. The governing Table 2B range is 0.5-1.25 points for PS4_Supporting, so 0.50 >= 0.5? yes; PS4 is met at Supporting strength. The available paper review did not verify the exact variant in the two literature leads, so the score rests on the two COSMIC occurrences and should receive human confirmation that they are separate qualifying tumor samples and not normal-tissue records.

VCEP rule

Points are assigned for phenotype according to (Table 2A). Phenotype criteria can only be used if the variant is absent from controls (PM2). Strength of evidence is determined by points according to (Table 2B). PS4_Supporting = .5-1.25 points ... **Presence of this variant in a tumor sample (databases such as COSMIC can be used)** 0.25

Evidence considered

• ClinGen Brain Malformations VCEP specification, Table 2A: 'Presence of this variant in a tumor sample (databases such as COSMIC can be used)' is scored 0.25 points per occurrence; the same table permits separate primary tumors to count as separate occurrences and limits tumor evidence to Supporting strength.
• COSMIC record COSV55912324 for PIK3CA c.1037T>G reports somatic_count = 2; calculation performed: 2 x 0.25 = 0.50 points.
• ClinGen Brain Malformations VCEP specification, Table 2B: PS4_Supporting = 0.5-1.25 points; explicit comparison: 0.50 >= 0.5? yes.
• The case evidence reports the exact variant absent from gnomAD v2.1 and gnomAD v4.1, providing the available PM2 prerequisite required by the PS4 rule.
• PMID:27631024 was selectively read from its extracted full text; the paper reports a cohort of 181 individuals with brain and body overgrowth but does not mention c.1037T>G, p.Val346Gly, or p.V346G, so it contributes no exact-variant case count.
• PMID:23946963 was listed as a literature lead for PS4, but no abstract or full text was available in the case materials; no exact-variant case count could be verified.

Still missing

• No exact c.1037T>G, p.Val346Gly, or p.V346G entry was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; the file supplies the governing rule and tables, not a variant-specific assignment.
• PM2 is supported by absence from gnomAD v2.1 and v4.1, but gnomAD-Canada was unavailable because the query timed out.
• The two COSMIC occurrences require human confirmation as separate qualifying tumor samples under Table 2A.
• PMID:23946963 had no abstract or full text available in the case materials, and PMID:27631024 did not mention the exact variant.

Sources

Reasoning

The VCEP limits PM1_Supporting to residues affecting critical functional domains in Table 4. The authoritative PIK3CA domain table lists kinase domains at amino acids 322-483 and 797-1068; residue 346 lies within 322-483. Therefore PM1 is met at Supporting strength without requiring a separate hotspot finding.

VCEP rule

Residues affecting critical functional domains provided in Table 4 for each gene.

Evidence considered

• ClinGen Brain Malformations VCEP Table 4/domain table: PIK3CA kinase domains are 322-483 and 797-1068; p.Val346Gly affects residue 346, within 322-483.
• The VCEP PM1 rule specifies Supporting strength for residues affecting critical functional domains provided in Table 4 for each gene; the VCEP index states PM1_Supporting is domain-based and does not require hotspot recurrence within an approved domain.

Sources

Reasoning

The governing VCEP PM2 rule awards supporting evidence for a variant absent or rare from controls in an ethnically matched cohort population sample (≥1). The variant was absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, satisfying the VCEP's absent-from-controls requirement with multiple population datasets. The governing VCEP file was searched for c.1037T>G, p.Val346Gly, and p.V346G with no variant-specific entry found.

VCEP rule

Absent/rare from controls in an ethnically-matched cohort population sample ( ≥1).

Evidence considered

• The VCEP CSPEC entry specifies PM2 at Supporting strength for a variant absent or rare from controls in an ethnically-matched cohort population sample (≥1).
• The exact variant was reported absent from gnomAD v2.1 and gnomAD v4.1, with search_status 'absent' and no source_data frequency or allele-count record.
• The exact variant was also reported absent from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer; these additional control subsets likewise contain no observation.

Still missing

• No entry for c.1037T>G, p.Val346Gly, or p.V346G was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.

Sources

Reasoning

The governing VCEP BA1 threshold is allele frequency >0.0926%. The variant was absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, so no allele frequency above the BA1 threshold is present. The governing VCEP file was searched for c.1037T>G, p.Val346Gly, and p.V346G with no variant-specific entry found.

VCEP rule

Allele frequency (>0.0926%). An allele frequency (>0.0926%) was approved. Note: this was adjusted from ACMG Guidelines due to maintaining the 5x threshold for benign (consistent with previously established guidelines)

Evidence considered

• The VCEP CSPEC entry for BA1 specifies allele frequency >0.0926% as the stand-alone threshold.
• The exact variant was reported absent from gnomAD v2.1 and gnomAD v4.1; both records have search_status 'absent' and no source_data frequency or allele-count record.
• The exact variant was also reported absent from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer; no population frequency above the BA1 threshold was observed.

Still missing

• No entry for c.1037T>G, p.Val346Gly, or p.V346G was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.

Sources

Reasoning

The governing VCEP BS1 threshold is allele frequency >0.0185%. The variant was absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, so the available population data do not exceed the BS1 threshold. The governing VCEP file was searched for c.1037T>G, p.Val346Gly, and p.V346G with no variant-specific entry found.

VCEP rule

Allele frequency (>0.0185%). An allele frequency (>0.0185%) was approved. (Supplemental Table 3).

Evidence considered

• The VCEP CSPEC entry for BS1 specifies allele frequency >0.0185% and identifies Supplemental Table 3 as the approval source.
• The exact variant was reported absent from gnomAD v2.1 and gnomAD v4.1; both records have search_status 'absent' and no source_data frequency or allele-count record.
• The exact variant was also reported absent from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer, providing no frequency above the BS1 threshold.

Still missing

• No entry for c.1037T>G, p.Val346Gly, or p.V346G was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.

Sources

Reasoning

The governing VCEP BS2 rule requires at least 3 homozygotes in gnomAD or at least 3 heterozygous occurrences in well-phenotyped family members. The variant was absent from gnomAD v2.1, v4.1, and the available non-cancer subsets, and the case evidence contains no qualifying family observations; therefore the required count is not met. The governing VCEP file was searched for c.1037T>G, p.Val346Gly, and p.V346G with no variant-specific entry found.

VCEP rule

Award BS2 if ≥3 homozygotes present in gnomAD or ≥3 heterozygous in well phenotyped family members. Clinical laboratories are encouraged to accumulate more than 2 (≥3) instances of well phenotyped family members before applying this strong criterion. To be considered for this point, the variant should be either germline (most common), or somatic in a relevant tissue. Homozygous occurrences in gnomAD or ExAC can also be counted for this point (≥3).

Evidence considered

• The VCEP CSPEC entry for BS2 requires ≥3 homozygotes in gnomAD or ≥3 heterozygous occurrences in well-phenotyped family members.
• The exact variant was reported absent from gnomAD v2.1 and gnomAD v4.1, with no homozygote observations; it was also absent from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer.
• No well-phenotyped family-member observations meeting the VCEP count requirement are present in the available case evidence.

Still missing

• No entry for c.1037T>G, p.Val346Gly, or p.V346G was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.

Sources

Reasoning

The VCEP applies PS1 as originally described: the variant must have the same amino-acid change as a previously established pathogenic variant, regardless of nucleotide change. Searches of the governing full-text file for c.1037T>G, p.Val346Gly, and p.V346G found no entry, and the available exact ClinVar record is classified Likely pathogenic rather than an independently established pathogenic comparator. No qualifying same-amino-acid pathogenic variant with a different nucleotide change is available in the reviewed evidence.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• ClinGen Brain Malformations VCEP specification: PS1 is listed as applicable as originally described; its governing text states that PS1 requires the same amino-acid change as a previously established pathogenic variant regardless of nucleotide change.
• The governing VCEP full-text file had no searchable entry for c.1037T>G, p.Val346Gly, or p.V346G.
• ClinVar exact record NM_006218.4:c.1037T>G (p.Val346Gly) is Likely pathogenic, single submitter, not an independently established pathogenic comparator with a different nucleotide change.

Still missing

• No c.1037T>G, p.Val346Gly, or p.V346G entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PIK3CA/fulltext/clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
• A qualifying pathogenic PIK3CA variant producing the same Val346Gly amino-acid change through a different nucleotide change was not identified.

Sources

Reasoning

The VCEP PS2 rule requires detectable variant allele fraction in an affected proband, absence from parental samples with confirmed maternity and paternity, and, for PS2_Strong, comparison showing the variant at a detectable fraction in affected tissue but absent or at a lower fraction in another tissue. The available case evidence does not provide proband-level allele fractions, parental test results or maternity/paternity confirmation, affected-tissue testing, cross-tissue allele fractions, or family-history information. The literature extraction for PMID:27631024 explicitly states that p.Val346Gly was not mentioned and provides no segregation or clinical data for this variant. Therefore PS2 cannot be evaluated.

VCEP rule

Award the PS2_Strong point if Criteria 1 AND Criteria 2 are fulfilled. Criteria 1: if the variant is present at a detectable allelic fraction in a proband with the disease but is absent from parental samples with confirmed maternity and paternity. Criteria 2: can be awarded if the variant is present at a detectable allele fraction in an affected tissue sample but is absent from or detected at a lower allelic fraction in another tissue (e.g. if present in 5% of brain tissue but absent from the blood or skin this point can be awarded). ... Award the PS2_Moderate point if Criteria 1 is fulfilled, OR if parents are not available but Criteria 2 is fulfilled.

Evidence considered

• ClinGen Brain Malformations VCEP specification v1.1, PS2 section: PS2_Strong requires Criteria 1 and Criteria 2; Criteria 1 requires a detectable allele fraction in a proband with the disease, absence from parental samples with confirmed maternity and paternity, and Criteria 2 concerns affected-tissue versus another-tissue allele fractions.
• The case bundle contains no proband-level parental-testing, maternity/paternity-confirmation, tissue-comparison, or family-history result for NM_006218.4:c.1037T>G (p.Val346Gly).
• PMID:27631024 paper extraction: the exact variant was not mentioned and the paper provided no clinical, segregation, or variant-specific data for p.Val346Gly.

Still missing

• No exact c.1037T>G, p.Val346Gly, or p.V346G notation was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; this governing file contains the rule but no variant-specific evidence row.
• Missing proband allele fraction, parental samples with confirmed maternity and paternity, affected-tissue allele fraction, comparison-tissue allele fraction, and family-history information.

Sources

Reasoning

No variant-specific functional assay result, assay controls, validation cohort, or quantitative functional readout for NM_006218.4:c.1037T>G (p.Val346Gly/p.V346G) was found in the case evidence. PMID:27631024 was reviewed through its extracted full-text finding and does not mention this variant or provide functional data for it. The VCEP permits PS3 only when the functional assay meets its specified acceptability criteria; the available evidence does not establish that condition or support any PS3 strength.

VCEP rule

Award PS3 if the functional assay meets the acceptability criteria delimited in (PMID: 31892348) with specifications added by the BMVCEP. Quality metrics and minimum validation controls required can be found in Supplementary Document 1.

Evidence considered

• ClinGen Brain Malformations VCEP specification v1.1, PS3 and Supplemental Document 1: the rule requires an acceptable functional assay; assays above supporting require positive and negative validation controls, with 8-34 variants for moderate and 35+ variants for strong evidence.
• PMID:27631024 extracted full-text finding: the paper does not explicitly mention PIK3CA c.1037T>G or p.Val346Gly and does not provide functional data for this variant.
• Searches of the governing VCEP full-text file for c.1037T>G, p.Val346Gly, and p.V346G returned no variant-specific entry.

Still missing

• The governing file clingen_brainmalform_acmg_specifications_v1_1.pdf contains no entry for c.1037T>G, p.Val346Gly, or p.V346G.
• A qualifying variant-specific functional study with documented assay controls, replicate information, and validation metrics is unavailable in the reviewed evidence.

Sources

Reasoning

The VCEP applies PM5 as originally described and requires a different missense change at the same amino-acid residue that has been determined to be pathogenic. The governing full-text file contains no entry for c.1037T>G, p.Val346Gly, or p.V346G, and the collected PM5 candidate set contains zero same-residue candidates; its retrieval also recorded an HTTP 429 error. The available evidence therefore does not establish that no qualifying Val346 comparator exists.

Rule

Missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• ClinGen Brain Malformations VCEP specification: PM5 is applicable as originally described and requires a missense change at an amino-acid residue where a different missense change determined to be pathogenic has been seen before.
• The governing VCEP full-text file had no searchable entry for c.1037T>G, p.Val346Gly, or p.V346G.
• The PM5 candidate collection reported zero same-residue candidates and an HTTP 429 retrieval error; this is insufficient to establish absence of a qualifying Val346 comparator.

Still missing

• No c.1037T>G, p.Val346Gly, or p.V346G entry was found in /Users/gs_agent/LYFESCI_HERMES_v11/vcep_db/PIK3CA/fulltext/clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.
• A complete independent search for pathogenic missense variants at PIK3CA residue 346 is still needed because PM5 candidate harvesting recorded HTTP Error 429: Too Many Requests.

Sources

Reasoning

The VCEP-specific PP2 rule requires the PIK3CA missense-constraint z-score to be greater than 3.09. The reviewed case evidence provides no ExAC or gnomAD missense-constraint z-score, so the stated threshold cannot be evaluated.

VCEP rule

Missense constraint computed in ExAC/gnomAD was utilized. Award PP2 if the z-score > 3.09. (applicable to MTOR, PIK3CA and AKT3 but not PIK3R2).

Evidence considered

• ClinGen Brain Malformations VCEP PP2 rule: for PIK3CA, award PP2 if the ExAC/gnomAD missense-constraint z-score is greater than 3.09.
• The case evidence contains no PIK3CA missense-constraint z-score from ExAC or gnomAD.

Still missing

• No ExAC/gnomAD missense-constraint z-score for PIK3CA was present in the reviewed case evidence.

Sources

Reasoning

No variant-specific functional assay demonstrating no damaging effect was identified, and no assay controls, validation cohort, or quantitative benign functional result for NM_006218.4:c.1037T>G (p.Val346Gly/p.V346G) was available. PMID:27631024 was reviewed through its extracted full-text finding and does not mention this variant or provide functional data for it. Therefore the VCEP quality-metric and minimum-control requirements for BS3 cannot be evaluated, so no benign strength is assigned.

VCEP rule

Follow recommendations set forth by the SVI in conjunction with specifications added by the Brain Malformation Group for quality metrics and minimum validation controls required (PMID: 31892348) (Supplementary Document 1)

Evidence considered

• ClinGen Brain Malformations VCEP specification v1.1, BS3: assessment follows SVI recommendations with Brain Malformation Group quality metrics and minimum validation controls.
• PMID:27631024 extracted full-text finding: the paper does not explicitly mention PIK3CA c.1037T>G or p.Val346Gly and does not provide functional data for this variant.
• Searches of the governing VCEP full-text file for c.1037T>G, p.Val346Gly, and p.V346G returned no variant-specific entry.

Still missing

• The governing file clingen_brainmalform_acmg_specifications_v1_1.pdf contains no entry for c.1037T>G, p.Val346Gly, or p.V346G.
• A qualifying variant-specific functional study showing no damaging effect, with documented controls and validation metrics, is unavailable in the reviewed evidence.

Sources

Reasoning

The VCEP permits BP2 at Supporting strength when the variant is observed in cis or trans with a known pathogenic variant in the same gene. The available case evidence does not document phase, a second pathogenic PIK3CA variant, or an affected-proband observation establishing such a cis/trans relationship, so BP2 cannot be assessed.

VCEP rule

Observed in cis or trans with a known pathogenic variant in the same gene.

Evidence considered

• vcep_materials.json, BP2 entry: the governing rule is "Observed in cis or trans with a known pathogenic variant in the same gene."
• The case bundle documents NM_006218.4:c.1037T>G / p.Val346Gly but contains no documented second pathogenic PIK3CA variant, parental/offspring phase result, or cis/trans observation for this variant.
• clingen_brainmalform_acmg_specifications_v1_1.pdf.txt was searched for c.1037T>G, p.Val346Gly, and p.V346G; no exact variant entry was found.

Still missing

• No c.1037T>G, p.Val346Gly, or p.V346G entry was found when clingen_brainmalform_acmg_specifications_v1_1.pdf.txt was searched; this file-search result does not establish whether case-level phase evidence exists.
• The available case evidence does not identify a second pathogenic PIK3CA variant with documented cis or trans phase relative to NM_006218.4:c.1037T>G.

Sources

Reasoning

The VCEP requires the variant to be observed in a case with an alternate molecular basis for disease in a different gene. The available case materials do not document such an exact-variant case or an alternate pathogenic molecular diagnosis, so BP5 cannot be evaluated.

VCEP rule

Brain Malformation Recommendation: Observed in a case with an alternate molecular basis for disease in a different gene

Evidence considered

• The VCEP BP5 modification requires observation in a case with an alternate molecular basis for disease in a different gene; no such case-level evidence is present in the available materials.

Still missing

• No exact c.1037T>G, p.Val346Gly, or p.V346G entry was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; the file supplies the governing rule and tables, not a variant-specific assignment.
• A case report or clinical record documenting this exact variant together with an alternate disease-causing variant in a different gene is unavailable.

Sources